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TitleStructure of the ATP-driven methyl-coenzyme M reductase activation complex.
Journal, issue, pagesNature, Vol. 642, Issue 8068, Page 814-821, Year 2025
Publish dateApr 16, 2025
AuthorsFidel Ramírez-Amador / Sophia Paul / Anuj Kumar / Christian Lorent / Sebastian Keller / Stefan Bohn / Thinh Nguyen / Stefano Lometto / Dennis Vlegels / Jörg Kahnt / Darja Deobald / Frank Abendroth / Olalla Vázquez / Georg Hochberg / Silvan Scheller / Sven T Stripp / Jan Michael Schuller /
PubMed AbstractMethyl-coenzyme M reductase (MCR) is the enzyme responsible for nearly all biologically generated methane. Its active site comprises coenzyme F, a porphyrin-based cofactor with a central nickel ion ...Methyl-coenzyme M reductase (MCR) is the enzyme responsible for nearly all biologically generated methane. Its active site comprises coenzyme F, a porphyrin-based cofactor with a central nickel ion that is active exclusively in the Ni(I) state. How methanogenic archaea perform the reductive activation of F represents a major gap in our understanding of one of the most ancient bioenergetic systems in nature. Here we purified and characterized the MCR activation complex from Methanococcus maripaludis. McrC, a small subunit encoded in the mcr operon, co-purifies with the methanogenic marker proteins Mmp7, Mmp17, Mmp3 and the A2 component. We demonstrated that this complex can activate MCR in vitro in a strictly ATP-dependent manner, enabling the formation of methane. In addition, we determined the cryo-electron microscopy structure of the MCR activation complex exhibiting different functional states with local resolutions reaching 1.8-2.1 Å. Our data revealed three complex iron-sulfur clusters that formed an electron transfer pathway towards F. Topology and electron paramagnetic resonance spectroscopy analyses indicate that these clusters are similar to the [8Fe-9S-C] cluster, a maturation intermediate of the catalytic cofactor in nitrogenase. Altogether, our findings offer insights into the activation mechanism of MCR and prospects on the early evolution of nitrogenase.
External linksNature / PubMed:40240609 / PubMed Central
MethodsEM (single particle)
Resolution2.14 - 2.78 Å
Structure data

19787

8s7v

EMDB-19787, PDB-8s7v:
Methyl-coenzyme M reductase activation complex binding to the A2 component
Method: EM (single particle) / Resolution: 2.56 Å

19788

8s7x

EMDB-19788, PDB-8s7x:
Methyl-coenzyme M reductase activation complex without the A2 component
Method: EM (single particle) / Resolution: 2.78 Å

51767

9h1l

EMDB-51767, PDB-9h1l:
Methyl-coenzyme M reductase activation complex binding to the A2 component after incubation with ATP
Method: EM (single particle) / Resolution: 2.14 Å

Chemicals

ChemComp-SHT:
O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE

ChemComp-TP7:
Coenzyme B

ChemComp-COM:
1-THIOETHANESULFONIC ACID

ChemComp-F43:
FACTOR 430

ChemComp-S5Q:
FeFe cofactor

ChemComp-ZN:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

Source
  • methanococcus maripaludis (archaea)
KeywordsOXIDOREDUCTASE / Methyl-coenzyme M reductase / activation complex / ATPase / Iron-sulfur clusters

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